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epi2me-labs / wf-amplicon

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add compatibility with dna_r9.4.1_e8_sup@v3.6 ? #25

Open ChristopherRichie opened 3 days ago

ChristopherRichie commented 3 days ago

Is your feature related to a problem?

the latest dorado basecaller config for r9.4.1 is dna_r9.4.1_e8_sup@v3.6 the available basecallers in current version appear to go up to dna_r9.4.1_e8_sup@v3.3.

thanks

Describe the solution you'd like

add dna_r9.4.1_e8_sup@v3.6 to the "override basecaller cfg" list

Describe alternatives you've considered

using older models for basecalling just because the latest is not integrated into wf-amplicon

Additional context

thanks!

cjw85 commented 3 days ago

The override list is simply the list of models which are supported by medaka for consensus and variant calling. Medaka does not support the 3.6 models and so they do not appear in the list.

The list is intended for the case where the requisite meta information is missing or corrupt in the input files. As you have found it can be abused to force the use of a particular, not necessarily appropriate, model.